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quick:start [2019/07/04 09:58]
ccrosby [Example interactive job request] 		quick:start [2026/06/11 11:17] (current)
kevin [Logging in for the First Time]
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 This guide is intended for experienced HPC users and provides a summary of the essential components of the systems available at the CHPC.  For more detailed information on the subjects below see the full [[guide:start|User Guide]]. This guide is intended for experienced HPC users and provides a summary of the essential components of the systems available at the CHPC.  For more detailed information on the subjects below see the full [[guide:start|User Guide]].
- 
-**NOTE: the new system is still under construction and information here and in the User Guide is incomplete and subject to sudden change.** 
  
 //docti cave// //docti cave//
  
 +
 +==== Video tutorials for newcomers ====
 +If you are a new user to the CHPC, please watch these videos:
 +  * [[https://youtu.be/fCM8ZaFn4rs|Setting up a cluster password and logging in for the first time]]
 +  * [[https://youtu.be/CIEVMlrKXF4|The CHPC's service nodes and using the module system]]
 +  * [[https://youtu.be/mQjh8J_aMYU|Test running in an interactive PBS session]]
 +  * [[https://youtu.be/MEwi4uxM5hc|Running an application in batch mode under PBS]]
 +
 +====Mailing List====
 +
 +The **[[https://lists.chpc.ac.za/sympa/info/chpc-users|chpc-users mailing list]]** is the primary communication channel for information about the status of the cluster.  [[https://lists.chpc.ac.za/sympa/subscribe/chpc-users|Subscribe here]] to receive new messages; and //please note you should check your various mail folders including **spam**.// Once subscribed and logged in, you will also be able to view the [[https://lists.chpc.ac.za/sympa/arc/chpc-users|archive]] of past messages.
  
  
 =====Overview: 32 832 cores===== =====Overview: 32 832 cores=====
-The CHPC's brand new Dell Linux cluster is up and running.+The CHPC's Dell Linux cluster has been up and running since 2014.
  
-The new system is an homogeneous cluster, comprising Intel 5th generation CPUs. As of March 2017 it has 1368 compute nodes with 24 cores and 128 GiB* memory (360 nodes have only 64 GiB) each, and five large memory "fat" nodes with 56 cores and 1TiB* each, all interconnected using FDR 56 Gb/s InfiniBand accessing 4 PB of shared storage over the Lustre filesystem. +The new system is an homogeneous cluster, comprising Intel 5th generation CPUs. As of May 2025 it has 41 nodes with 24 cores and 256 GiB memory, 784 compute nodes with 24 cores and 128 GiB* memory, 355 nodes with 24 cores and 64 GiB memory, and four large memory "fat" nodes with 56 cores and 1TiB* each, all interconnected using FDR 56 Gb/s InfiniBand accessing 4 PB of shared storage over the Lustre filesystem. 
  
  
-* Maximum available memory on each type of node: ''mem=125gb'' (regular) or ''mem=61gb'' (regular with only 64GiB), and ''mem=1007gb'' (fat).+* Maximum available memory on each type of node: ''mem=250gb'' (regular with 256 GiB), ''mem=124gb'' (regular with 128 GiB) or ''mem=61gb'' (regular with only 64GiB), and ''mem=1007gb'' (fat).
  
  
 ====GPU nodes==== ====GPU nodes====
  
-There are 9 compute nodes that contain a total of 24 Nvidia V100 GPUs.  For more information see the [[guide:gpu|GPU guide]].+There are 9 compute nodes that contain a total of 30 Nvidia V100 GPUs.  For more information see the [[guide:gpu|GPU guide]].
 =====Logging in===== =====Logging in=====
  
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 </code> </code>
  
 +====Logging in for the First Time====
  
-The new system is running CentOS 7.0 and uses the //Bash// shell by default. +:!: You will use a password only for the **first time** you log in using ssh. And the first step will be to set up your ssh key.  After this, you **can only log in using ssh keys and your password will be disabled.**
  
-You should change your password after logging in the first time. +Please read carefully and follow the procedure to set up your [[guide:sshkeys|ssh keys]] for your first login [[guide:sshkeys|here]].
-To change your password, use the ''passwd'' command. +
-Rules are: 10 characters, with at least one of the following character types: upper and lower case, numbers, and special characters.  Use ssh keys wherever possible.+
  
-====scp/rsync==== 
  
-To transfer data onto or off the CHPC cluster use **scp** or **rsync** comands and connect to or from the cluster's scp node: **''scp.chpc.ac.za''**.  **Please do not transfer files directly to lengau.chpc.ac.za.**  It is a shared login node, and in order not to overload it, file transfer should be done to the dedicated scp server.  For the same reason, when copying large files from one directory to another, it is preferable to not do this on the login node.  You can log into one of several other servers to do the copying:+====Long Interactive Sessions==== 
 + 
 +Once you have logged in, give some consideration to how you will be using your session on the login node.  If you are going to spend a long time logged in, doing a variety of tasks, it is best to get yourself **[[http://wiki.chpc.ac.za/quick:start#example_interactive_job_request|an interactive PBS session]]** to work in.  This way, if you need to do something demanding, it will not conflict with other users logged into the login node. 
 + 
 +The new system is running [[quick:os|CentOS]] 7.3 and uses the //Bash// shell by default.  
 + 
 +====Trouble Logging in?==== 
 +Many users have their login blocked at some point. Usually this is because an incorrect password was entered more times than permitted (5 times). This restriction was put in place to prevent brute-force attacks by malicious individuals who want to gain access to your account. 
 + 
 +  * If you cannot log in, the first step is to make sure that you typed your username, hostname (lengau.chpc.ac.za or scp.chpc.ac.za) and password correctly. It sounds stupid, but this is often the problem. It happens to CHPC staff too... 
 +  * Next, check that you are not experiencing a network problem. If you see a message along the lines of "cannot resolve hostname", then your network is probably at fault (assuming that your spelling is correct). 
 +  * If your network connection is fine, wait 30 minutes before attempting to log in again. After this period, the block is supposed to be automatically removed. 
 +  * If for some reason this does not work, you should go to your user page on users.chpc.ac.za. There is a link at that address, to the left, which allows you to change your password and also edit other details for your entry on our user database (email addresses, qualifications, institution, etc.) **Be sure that your password conforms to all requirements** 
 +  * If even changing the password does not help, please contact our helpdesk, and ask for our assistance. 
 + 
 + 
 +==== Transferring Data ==== 
 +There are two main protocols for transferring data to and from the CHPC: 
 + 
 +=== Globus === 
 +Globus is a set of tools built on the GridFTP protocol.  Instructions for transferring data with Globus are provided [[howto:globus|here]]. 
 + 
 +=== scp === 
 + 
 +To transfer data onto or off the CHPC cluster use **scp**, **rsync** or sftp commands and connect to or from the cluster's scp node: **''scp.chpc.ac.za''**.  **Please do not transfer files directly to lengau.chpc.ac.za.**  It is a shared login node, and in order not to overload it, file transfer should be done to the dedicated scp server.  For the same reason, when copying large files from one directory to another, it is preferable to not do this on the login node.  You can log into one of several other servers to do the copying:
   * Use an [[http://wiki.chpc.ac.za/quick:start?s[]=interactive#example_interactive_job_request|Interactive PBS session]] on a compute node   * Use an [[http://wiki.chpc.ac.za/quick:start?s[]=interactive#example_interactive_job_request|Interactive PBS session]] on a compute node
   * ssh into scp   * ssh into scp
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 subdirectory of your scratch directory ///mnt/lustre/users/yourusername///   subdirectory of your scratch directory ///mnt/lustre/users/yourusername///  
 (where //yourusername// is replaced by your user name on the CHPC cluster). (where //yourusername// is replaced by your user name on the CHPC cluster).
 +
 +
 +=== Downloading files from other servers ===
 +You may need to download data from a server at another site.  Do not do this on ** //login2// **!  Use ** // scp.chpc.ac.za// ** for this purpose.  The easiest way of doing this is with the **wget** command:
 +
 +<code>
 +wget http://someserver.someuni.ac.za/pub/somefile.tgz
 +</code>
 +
 +Very large files may be transferred more quickly by using a multi-threaded downloader. The easiest of these is **axel**, see [[https://github.com/axel-download-accelerator/axel|axel's GitHub page]].  The syntax is very simple:
 +
 +<code>
 +module load chpc/compmech/axel/2.17.6
 +axel -n 4 -a http://someserver.someuni.ac.za/pub/somefile.tgz
 +</code>
 +
 +
  
 [[guide:connect|Read more on connecting to the CHPC...]] [[guide:connect|Read more on connecting to the CHPC...]]
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 ^ Mount point  ^  File System ^  Size ^  Quota ^  Backup ^ Access  ^ ^ Mount point  ^  File System ^  Size ^  Quota ^  Backup ^ Access  ^
-| ''/home''  | NFS  | 80 TB  | **15 GB**  | Yes  | Yes  |  +| ''/home''  | NFS  | 80 TB  | **45 GB**  | NO <sup>[1]</sup>  | Yes  |  
-| ''/mnt/lustre/users''  | Lustre  | 4 PB  | none  | NO  | Yes  |  +| ''/mnt/lustre/users''  | Lustre  | 4 PB  | none :!:  | NO  | Yes   |  
-| ''/lustre/SCRATCH5''  | Lustre  | 1 PB  | none  | NO  | **//No longer available//**  |  +| ''/apps''  | NFS  | 20 TB  | none  | Yes  | No <sup>[2]</sup>  |  
-| ''/apps''  | NFS  | 20 TB  | none  | Yes  | On request  |  +| ''/mnt/lustre/groups''  | Lustre  | 1 PB  | 1 TB <sup>[3]</sup>| NO  | On request only  | 
-| ''/mnt/lustre/groups''  | Lustre  | 1 PB  | none  | NO  | On request only  | +
  
 +:!: **IMPORTANT NOTE:** Files older than 90 days on ''/mnt/lustre/users'' will be automatically deleted without any warning or advance notice.
 +
 +**Note [1]** Unfortunately, at the moment the CHPC cannot guarantee any backup of the ''/home'' file system owing to hardware limitations.
 +
 +**Note [2]** Create a support ticket on Helpdesk if you would like to request us to install a new application, library or programming tool.
 +
 +**Note [3]** Access to ''/mnt/lustre/groups'' is by application only and a quota will be assigned to the programme, to be shared by all members of that group.
 +
 +It is essential that all files that your job script writes to be on Lustre, apart from scheduler errors you will lose performance because your home directory is on NFS which is not a parallel file system. It is also recommended that all files your jobs scripts reads, especially if large or read more than once, be on Lustre for the same reason.
 +
 +It is usually okay to keep binaries and libraries on home since they are read once and loaded into RAM when your executable launches. But you may notice improved performance if they are also on Lustre.
 ====Quotas==== ====Quotas====
  
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 The module command may be abbreviated and optionally be given a search term, eg.:   The module command may be abbreviated and optionally be given a search term, eg.:  
   module ava chpc/open   module ava chpc/open
 +Or, more flexibly, you can pipe stderr to grep, and search for a phrase, such as mpi:
 +  module avail 2>&1 | grep mpi
 To see a synopsis of a particular modulefile's operations: To see a synopsis of a particular modulefile's operations:
   module help <module_name>   module help <module_name>
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 ''workq'' is no longer to be used. ''workq'' is no longer to be used.
  
-The available queues are:+The available queues with their nominal parameters are given in the following table.  Please take note that these limits may be adjusted dynamically to manage the load on the system.
  
 ^ Queue Name  ^ Max. cores  ^ Min. cores  ^  Max. jobs  ^^  Max. time  ^  Notes  ^ Access  ^ ^ Queue Name  ^ Max. cores  ^ Min. cores  ^  Max. jobs  ^^  Max. time  ^  Notes  ^ Access  ^
 ^ :::  ^  per job  ^^  in queue  ^  running  ^  hrs  ^ :::  ^ :::  ^ ^ :::  ^  per job  ^^  in queue  ^  running  ^  hrs  ^ :::  ^ :::  ^
-| serial  |  23 |  1 |  ??? |  ??? |  48 | For single-node non-parallel jobs.  |  | +| serial  |  23 |  1 |  24 |  10 |  48 | For single-node non-parallel jobs.  |  | 
-| seriallong  |  12 |  1 |  ??? |  ??? |  144 | For very long sub 1-node jobs.  |  |+| seriallong  |  12 |  1 |  24 |  10 |  144 | For very long sub 1-node jobs.  |  |
 | smp  |  24 |  24 |  20 |  10 |  96 | For single-node parallel jobs.  |  | | smp  |  24 |  24 |  20 |  10 |  96 | For single-node parallel jobs.  |  |
-^ normal  ^  240 ^  48 ^  20 ^  10 ^  48 ^ The standard queue for parallel jobs ^  ^ +^ normal  ^  240 ^  25 ^  20 ^  10 ^  48 ^ The standard queue for parallel jobs ^  ^ 
-| large  |  2400 |  264 |  10 |  5 |  48 | For large parallel runs  | //Restricted//  |+| large  |  2400 |  264 |  10 |  5 |  96 | For large parallel runs  | //Restricted//  | 
 +| xlarge  |  6000 |  2424 |  2 |  1 |  96 | For extra-large parallel runs  | //Restricted//  |
 | express  |  2400 |  25 |  N/A |  100 total nodes |  96 | For paid commercial use only  | //Restricted//  | | express  |  2400 |  25 |  N/A |  100 total nodes |  96 | For paid commercial use only  | //Restricted//  |
 | bigmem  |  280 |  28 |  4 |  1 |  48 | For the large memory (1TiB RAM) nodes. | //Restricted//  | | bigmem  |  280 |  28 |  4 |  1 |  48 | For the large memory (1TiB RAM) nodes. | //Restricted//  |
 | vis  |  12 |  1 |  1 |  1 |  3 | Visualisation node  |  | | vis  |  12 |  1 |  1 |  1 |  3 | Visualisation node  |  |
 | test  |  24 |  1 |  1 |  1 |  3 | Normal nodes, for testing only  |  | | test  |  24 |  1 |  1 |  1 |  3 | Normal nodes, for testing only  |  |
 +| gpu_1 |  10 |  1 |    |  2 |  12 | Up to 10 cpus, 1 GPU        |  |
 +| gpu_2 |  20 |  1 |    |  2 |  12 | Up to 20 cpus, 2 GPUs        |  |
 +| gpu_3 |  36 |  1 |    |  2 |  12 | Up to 36 cpus, 3 GPUs        |  |
 +| gpu_4 |  40 |  1 |    |  2 |  12 | Up to 40 cpus, 4 GPUs        |  |
 +| gpu_long |  20 |  1 |    |  1 |  24 | Up to 20 cpus, 1 or 2 GPUs        |  //Restricted//  |
 +
 +
  
 ===Notes:=== ===Notes:===
  
 +  * The queue limits may be adjusted dynamically in order to best manage the workload on the system.  Use the command ''qstat -Qf'' to see what the current limits are.
   * A standard compute node has 24 cores and 128 GiB of memory (RAM).   * A standard compute node has 24 cores and 128 GiB of memory (RAM).
   * Each large memory node has 56 cores and 1 TiB of memory.   * Each large memory node has 56 cores and 1 TiB of memory.
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 <code bash> <code bash>
 #!/bin/bash #!/bin/bash
-#PBS -l ncpus=24:mpiprocs=24:nodetype=haswell_reg+#PBS -l select=1:ncpus=24:mpiprocs=24
 #PBS -P PRJT1234 #PBS -P PRJT1234
 #PBS -q smp #PBS -q smp
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 #PBS -e /mnt/lustre/users/USERNAME/OMP_test/test1.err #PBS -e /mnt/lustre/users/USERNAME/OMP_test/test1.err
 #PBS -m abe #PBS -m abe
-#PBS -M your.email@address+#PBS -M youremail@ddress
 ulimit -s unlimited ulimit -s unlimited
  
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 #PBS -e /mnt/lustre/users/USERNAME/WRF_Tests/WRFV3/run2km_100/wrf.err #PBS -e /mnt/lustre/users/USERNAME/WRF_Tests/WRFV3/run2km_100/wrf.err
 #PBS -m abe #PBS -m abe
-#PBS -M your.email@address+#PBS -M youremail@ddress
 ulimit -s unlimited ulimit -s unlimited
 . /apps/chpc/earth/WRF-3.7-impi/setWRF . /apps/chpc/earth/WRF-3.7-impi/setWRF
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